This study uses the historical-critical method. The purpose of this study is to uncover the pedagogy of pesantren, including the education model in pesantren and the dynamics of pesantren in responding to contemporary issues. The result of the study shows that pesantren has pedagogical concepts that integrate science with the art of teaching. There are various methods and strategies of the pesantren pedagogy which are maintained until today, and they can be a model of the educational system in the Indonesian archipelago as they have contributed to humanity and built peace. In addition, in responding to contemporary issues, pesantren has participated in building a democratic society, encouraging awareness of gender equality, improving public service quality, and promoting paradigm shift within pesantren, i.e. integrative pesantren.